It appears that any natural blocks in the world that is over the height of 64 blocks do not regenerate, this makes any region in Athena unable to regenerate it's natural blocks in a nightly restart. Here are a few examples from the Revenants Clay & Sand mines near Beswin:

There is also the problem of player derp blocks around the regions, those do not regenerate ever and require manual removal, any dents in the geology and it stays forever.